You need to install EB 1.2 to the same target as EB 1.1.

Delete the EB folder inside your EB folder and reinstall EB 1.2.

If you have installed EB 1.1 to "...\Rome - Total War"
then you'll have to install EB 1.2 also to "...\Rome - Total War"

And NOT to "...\Rome - Total War\EB" as you probably have done.